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- PDB-2i60: Crystal structure of [Phe23]M47, a scorpion-toxin mimic of CD4, i... -

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Basic information

Entry
Database: PDB / ID: 2i60
TitleCrystal structure of [Phe23]M47, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 GP120 envelope glycoprotein and anti-HIV-1 antibody 17B
Components
  • (ANTIBODY 17B ...) x 2
  • EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)
  • [PHE23]M47, SCORPION-TOXIN MIMIC OF CD4
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / GP120 / YU2 / scorpion toxin / CD4 mimic / [Phe23]M47 / antibody / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsHuang, C.-C. / Kwong, P.D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Combinatorial optimization of a CD4-mimetic miniprotein and cocrystal structures with HIV-1 gp120 envelope glycoprotein.
Authors: Stricher, F. / Huang, C.C. / Descours, A. / Duquesnoy, S. / Combes, O. / Decker, J.M. / Kwon, Y.D. / Lusso, P. / Shaw, G.M. / Vita, C. / Kwong, P.D. / Martin, L.
History
DepositionAug 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 6, 2012Group: Structure summary
Revision 1.4Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE A SEQUENCE DATABASE REFERENCE FOR ENTITIES 2, 3 AND 4 DOES NOT CURRENTLY EXIST

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)
L: ANTIBODY 17B LIGHT CHAIN
H: ANTIBODY 17B HEAVY CHAIN
M: [PHE23]M47, SCORPION-TOXIN MIMIC OF CD4
P: EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)
Q: ANTIBODY 17B LIGHT CHAIN
R: ANTIBODY 17B HEAVY CHAIN
S: [PHE23]M47, SCORPION-TOXIN MIMIC OF CD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,94326
Polymers171,2838
Non-polymers3,66018
Water8,737485
1
G: EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)
L: ANTIBODY 17B LIGHT CHAIN
H: ANTIBODY 17B HEAVY CHAIN
M: [PHE23]M47, SCORPION-TOXIN MIMIC OF CD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,47113
Polymers85,6424
Non-polymers1,8309
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)
Q: ANTIBODY 17B LIGHT CHAIN
R: ANTIBODY 17B HEAVY CHAIN
S: [PHE23]M47, SCORPION-TOXIN MIMIC OF CD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,47113
Polymers85,6424
Non-polymers1,8309
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.439, 157.765, 109.846
Angle α, β, γ (deg.)90.00, 93.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules LQHR

#2: Antibody ANTIBODY 17B LIGHT CHAIN


Mass: 23399.898 Da / Num. of mol.: 2 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus / Production host: Human herpesvirus 4 (Epstein-Barr virus)
#3: Antibody ANTIBODY 17B HEAVY CHAIN


Mass: 24457.387 Da / Num. of mol.: 2 / Fragment: ANTIGEN-BINDING FRAGMENT, FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Lymphocryptovirus / Production host: Human herpesvirus 4 (Epstein-Barr virus)

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Protein / Protein/peptide / Sugars , 3 types, 20 molecules GPMS

#1: Protein EXTERIOR MEMBRANE GLYCOPROTEIN(GP120) / HIV-1 YU2 GP120


Mass: 34838.691 Da / Num. of mol.: 2 / Fragment: CORE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: YU2 / Gene: Env / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P35961
#4: Protein/peptide [PHE23]M47, SCORPION-TOXIN MIMIC OF CD4


Mass: 2945.642 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This protein is a mimic of the protein that occurs naturally in Leiurus quinquestriatus hebraeus (Israeli scorpion)
Source: (synth.) synthetic construct (others)
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 487 molecules

#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ISOPROPANOL, SODIUM citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2004 / Details: Si (220)
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 67879 / % possible obs: 71.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.096 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.288 / % possible all: 19.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1YYM

1yym


Resolution: 2.4→19.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 363147.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 5788 10.2 %RANDOM
Rwork0.215 ---
obs0.215 56951 83.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4433 Å2 / ksol: 0.322487 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1--13.42 Å20 Å2-2.62 Å2
2--0.64 Å20 Å2
3---12.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11717 0 232 485 12434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.375 300 10.1 %
Rwork0.297 2685 -
obs--43.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3iso.pariso.top
X-RAY DIFFRACTION4water_rep.paramwater_rep.top

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